class: center, middle, inverse, title-slide .title[ # Hotspots del Vector del Dengue ] .author[ ### Felipe Antonio Dzul Manzanilla ] .date[ ### 2022: Last compiled 2022-10-27 ] --- class: left, top <style>.xe__progress-bar__container { top:0; opacity: 1; position:absolute; right:0; left: 0; } .xe__progress-bar { height: 0.25em; background-color: #0051BA; width: calc(var(--slide-current) / var(--slide-total) * 100%); } .remark-visible .xe__progress-bar { animation: xe__progress-bar__wipe 200ms forwards; animation-timing-function: cubic-bezier(.86,0,.07,1); } @keyframes xe__progress-bar__wipe { 0% { width: calc(var(--slide-previous) / var(--slide-total) * 100%); } 100% { width: calc(var(--slide-current) / var(--slide-total) * 100%); } }</style> <div> <style type="text/css">.xaringan-extra-logo { width: 110px; height: 228px; z-index: 0; background-image: url(https://www.gob.mx/cms/uploads/action_program/main_image/26942/post_post_portadavectores.gif); background-size: contain; background-repeat: no-repeat; position: absolute; top:1em;right:1em; } </style> <script>(function () { let tries = 0 function addLogo () { if (typeof slideshow === 'undefined') { tries += 1 if (tries < 10) { setTimeout(addLogo, 100) } } else { document.querySelectorAll('.remark-slide-content:not(.title-slide):not(.inverse):not(.hide_logo)') .forEach(function (slide) { const logo = document.createElement('div') logo.classList = 'xaringan-extra-logo' logo.href = null slide.appendChild(logo) }) } } document.addEventListener('DOMContentLoaded', addLogo) })()</script> </div> ### Ciclo de Vida del Programa de Prevención y Control del Dengue <div id="htmlwidget-6fab7b692ceff5b56f8a" style="width:100%;height:600px;" class="grViz html-widget"></div> <script type="application/json" data-for="htmlwidget-6fab7b692ceff5b56f8a">{"x":{"diagram":"digraph {\n\n # graph definitions\n graph [layout = dot, rankdir = TB]\n \n \n \n ###########\n # node definitions\n node [shape = circle, style = filled, color = black, fixedsize = true, width = 2] \n prog_den [label = \"Programa de Dengue\", fillcolor = \"#4285F4\", color = \"white\", fontcolor = \"white\"]\n #\n brote [label = \"Brote\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n control_probables [label = \"Control de Probables\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n \n node [shape = circle, style = filled, color = grey] \n irs [label = \"Rociado Residual\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n cl [label = \"Control Larvario\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n ovitraps [label = \"Ovitrampas\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n adult [label = \"Colecta de Adultos\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n enc_ver [label = \"Encuesta Verificación\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n plat [label = \"Plataforma\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n \n #########\n node [shape = rectangle, style = filled, color = black, fixedsize = true, width = 2.5] \n hotspots [label = \"Hotspots\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n #act [label = \"Casos Actuales\", fillcolor = \"darkorange\", color = \"white\", fontcolor = \"black\"]\n \n # Vigilancia epidemiológica\n epi [label = \"Vigilancia Epidemiológica\", fillcolor = \"#DB4437\", color = \"white\", fontcolor = \"white\"]\n \n #\n data_historic [label = \"Datos Históricos\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n data_datos_actuales [label = \"Datos Actuales\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n data_acumulados [label = \"Datos Acumulados\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n data_trans_activa [label = \"Transmisión Activa\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n \n \n ent [label = \"Vigilancia Entomológica\", fillcolor = \"#0F9D58\", color = \"white\", fontcolor = \"white\"]\n \n \n \n ind [label = \"Indicadores\", fillcolor = \"#0F9D58\", color = \"white\", fontcolor = \"black\"]\n ###################\n prog_den -> {epi, ent}[penwidth = 4]\n \n epi -> {data_historic data_datos_actuales}[penwidth = 4]\n data_datos_actuales -> {data_acumulados, data_trans_activa}[penwidth = 4]\n \n data_historic -> {hotspots}[penwidth = 4]\n \n data_trans_activa -> {control_probables}[penwidth = 4] \n data_acumulados -> {brote}[penwidth = 4] \n \n control_probables -> {plat}[penwidth = 4]\n brote -> {plat}[penwidth = 4]\n \n\n \n hotspots -> {\n cl[arrowhead = crow, arrowtail = box, color = \"Maroon\"]\n irs[arrowhead = crow, arrowtail = box, color = \"Maroon\"]\n } -> plat[penwidth = 4]\n \n ent -> {adult, ovitraps, enc_ver} -> plat[penwidth = 4] \n plat -> ind[penwidth = 4]\n ind -> prog_den[penwidth = 4]\n \n\n \n \n \n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script> --- ### Línea de Tiempo de la Vigilancia Epidemiológica & Entomológica <hr style="height:2px;border-width:0;color:#330019;background-color:#330019"> <div id="htmlwidget-b1a6bb4eba9485841cf9" class="timevis html-widget" style="width:100%;height:100%;"> <div class="btn-group zoom-menu"> <button type="button" class="btn btn-default btn-lg zoom-in" title="Zoom in">+</button> <button type="button" class="btn btn-default btn-lg zoom-out" title="Zoom out">-</button> </div> </div> <script type="application/json" data-for="htmlwidget-b1a6bb4eba9485841cf9">{"x":{"items":[{"start":"2008-01-01","end":"2022-10-27","content":"Vigilancia Epidemiológica Pasiva","style":"text-align: center; 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color: white; font-size: 12px; border-color: darkorange; border: 2px solid white; background-color: darkorange;","group":"4"},{"start":"2021-01-01","end":"2022-10-27","content":"Actuales (clusters de casos y cadenas de transmisión)","style":"text-align: left; font-weight: bold; color: white; font-size: 12px; border-color: darkorange; border: 2px solid white; background-color: darkorange;","group":"4"},{"start":"2021-03-01","end":"2022-10-27","content":"Transmisión Activa (Identificación de cadenas de transmisión: knox test)","style":"text-align: righ; font-weight: bold; color: white; font-size: 12px; border-color: darkorange; border: 2px solid white; background-color: darkorange;","group":"4"}],"groups":[{"id":"1","content":"Paciente","style":"text-align: center; font-weight: bold; color: white; font-size: 15px; border-color: #DB4437; border: 2px solid white; background-color: #DB4437;"},{"id":"2","content":"Vector","style":"text-align: center; font-weight: bold; color: white; font-size: 15px; border-color: #4285F4; border: 2px solid white; background-color: #4285F4;"},{"id":"3","content":"Virus-Vector","style":"text-align: center; font-weight: bold; color: white; font-size: 15px; border-color: #0F9D58; border: 2px solid white; background-color: #0F9D58;"},{"id":"4","content":"Análisis espacial","style":"vertical-align: middle; text-align: center; font-weight: bold; color: white; font-size: 20px; border-color: darkorange; border: 2px solid white; background-color: darkorange;"}],"showZoom":true,"zoomFactor":0.5,"fit":true,"options":[],"height":null,"timezone":null,"api":[]},"evals":[],"jsHooks":[]}</script> --- ### **Análisis Espacial del Vector del Dengue** <hr style="height:2px;border-width:0;color:#330019;background-color:#330019"> <div id="htmlwidget-302a7219fb2ea1aff814" style="width:100%;height:504px;" class="grViz html-widget"></div> <script type="application/json" data-for="htmlwidget-302a7219fb2ea1aff814">{"x":{"diagram":"digraph {\n # graph definitions\n graph [layout = dot, rankdir = TB]\n \n # node definitions\n node [shape = rectangle, \n style = filled, \n color = grey, \n nodesep = .5,\n fixedsize = true, \n width = 2.5] \n \n # edge definition\n edge [color = grey, arrowhead = normal, arrowtail = dot]\n \n ##### entomological data\n \n ento [label = \"Vigilancia Entomológica\", fillcolor = \"#FF5A5F\", color = \"white\", fontcolor = \"white\"]\n data_historic [label = \"Datos Históricos\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n \n years [label = \"2014-2019\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n data_datos_actuales [label = \"Datos del Año Actual\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n data_acumulados [label = \"Datos hasta la Semana Actual\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n data_trans_activa [label = \"Semana Actual\", fillcolor = \"gray\", color = \"white\", fontcolor = \"white\"]\n \n \n ##### Spatial Data\n \n geo_data [label = \"Geoestatistical Data\", fillcolor = \"#0F9D58\", color = \"white\", fontcolor = \"white\"]\n \n \n \n # Análisis \n spde [label = \"SPDE-INLA\", fillcolor = \"orange\", color = \"white\", fontcolor = \"black\"]\n hotspots [label = \"Hotspots Analysis\", fillcolor = \"orange\", color = \"white\", fontcolor = \"black\"]\n #prediction [label = \"Predicción Espacial de Huevos\", fillcolor = \"orange\", color = \"white\", fontcolor = \"black\"]\n \n # entomological study\n ovitraps [label = \"Ovitrampas\", fillcolor = \"orange\", color = \"white\", fontcolor = \"black\"]\n enc_ver [label = \"Encuesta-Verificación\", fillcolor = \"orange\", color = \"white\", fontcolor = \"black\"]\n adults [label = \"Colecta de Adultos\", fillcolor = \"orange\", color = \"white\", fontcolor = \"black\"]\n \n \n # software\n r_rstudio [label = \"R & RStudio\", fillcolor = \"DodgerBlue\", color = \"white\", fontcolor = \"white\"]\n deneggs [label = \"deneggs Package\", fillcolor = \"DodgerBlue\", color = \"white\", fontcolor = \"white\"] \n \n \n \n \n ##### define the relation\n \n \n ento -> {ovitraps enc_ver adults} \n \n {ovitraps adults} -> geo_data -> {data_historic data_datos_actuales}\n data_historic -> years\n \n data_datos_actuales -> {data_acumulados data_trans_activa}\n \n {years data_acumulados data_trans_activa} ->spde -> hotspots\n \n {hotspots} -> r_rstudio -> deneggs\n \n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script> --- ### **Análisis Espacial del Vector del Dengue** <hr style="height:2px;border-width:0;color:#330019;background-color:#330019"> <div id="htmlwidget-3928298e2b5e0c70b2b4" style="width:90%;height:500px;" class="grViz html-widget"></div> <script type="application/json" data-for="htmlwidget-3928298e2b5e0c70b2b4">{"x":{"diagram":"digraph {\n\n # graph definitions\n graph [layout = dot, rankdir = TB]\n \n # node definitions\n node [shape = rectangle, style = filled, color = grey] \n \n #\n cenaprece [label = \"CENAPRECE\", fillcolor = \"SeaGreen\", color = \"white\", fontcolor = \"white\"]\n ovitrap [label = \"Ovitrampas\", fillcolor = \"SeaGreen\", color = \"white\", fontcolor = \"white\"]\n coord [label = \"Coordenadas\", fillcolor = \"SeaGreen\", color = \"white\", fontcolor = \"white\"]\n ovicoord [label = \"ovi + coord\"]\n \n # flow chart for inegi\n inegi [label = \"INEGI\", fillcolor = \"DeepSkyBlue\", color = \"white\", fontcolor = \"black\"]\n loc [label = \"Localidades Shapefile\", fillcolor = \"DeepSkyBlue\", color = \"white\", fontcolor = \"black\"]\n\n ###\n mesh [label = \"1. Mesh\"]\n spde [label = \"2. SPDE\"]\n \n proj_train [label = \"3a. Projector Matrix A. Test\"]\n proj_test [label = \"3b. Projector Matrix A. Train\"]\n \n spatial_field [label = \"4. Spatial Field W\"]\n \n stack_train [label = \"5a. Stack Train\"]\n stack_test [label = \"5b. Stack Test\"]\n stack_pred [label = \"5c. Stack Prediction\"]\n stack_joint [label = \"6. Joint Stack\"]\n \n formula [label = \"7. Formula\"]\n inla [label = \"8. INLA\", fillcolor = \"Orange\", color = \"white\", fontcolor = \"white\"]\n \n \n \n # edge definitions with the node IDs\n edge [color = black]\n cenaprece -> {ovitrap, coord} -> ovicoord\n #\n inegi -> loc -> ovicoord\n #\n ovicoord -> mesh\n mesh -> spde -> spatial_field -> stack_joint\n spde -> {proj_train, proj_test}\n spatial_field -> {stack_test, stack_train, stack_pred} -> stack_joint -> formula -> inla \n proj_train -> stack_train\n proj_test -> stack_test\n\n \n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script> .tiny[.blue[.footnote[ [Modificado de Zuur et al 2017](http://www.highstat.com/index.php/beginner-s-guide-to-regression-models-with-spatial-and-temporal-correlation); [Dzul-Manzanilla et al 2019](http://acaentmex.org/entomologia/revista/2019/EMF/EMF%20497-501.pdf)]]] --- ### **Análisis Espacial del Vector del Dengue** <hr style="height:2px;border-width:0;color:#330019;background-color:#330019"> <div id="htmlwidget-b312d62c8b5408c4458c" style="width:90%;height:500px;" class="grViz html-widget"></div> <script type="application/json" data-for="htmlwidget-b312d62c8b5408c4458c">{"x":{"diagram":"digraph {\n\n # graph definitions\n graph [layout = dot, rankdir = TB]\n \n # node definitions\n node [shape = rectangle, style = filled, color = grey] \n \n #\n \n inla [label = \"8. INLA\", fillcolor = \"Orange\", color = \"white\", fontcolor = \"white\"]\n stat [label = \"9. Statistics\"]\n \n zeros [label = \"9.1. % Zeros\"]\n disp [label = \"9.2. Dispersion Statistics\"]\n dic [label = \"9.3. Deviance Information Criterio\"]\n pear [label = \"9.4. Pearson Residuals\"]\n \n ##\n p [label = \"Poisson\"]\n zip [label = \"ZeroInflated Poisson\"]\n nb [label = \"Negative Binomial\"]\n zinb [label = \"ZeroInflated Poisson Negative Binomial\"]\n \n sel [label = \"10.Select the Distribution & Model\"]\n \n # prediction ####\n ext_pred [label = \"11. Extract Index Prediction\"]\n coor_pred [label = \"12. Extract Coordinates Prediction\"]\n pred [label = \"13. Prediction\"]\n \n hotspots [label = \"14.Hotspots\", fillcolor = \"Orange\", color = \"white\", fontcolor = \"white\"]\n save [label = \"15. Save results\"]\n \n mappred [label = \"15a. Prediction Map\"]\n hotspotsb [label = \"15b. Hotspots\"]\n dics [label = \"15c. DICs\"]\n loc [label = \"15d. Locality\"]\n data [label = \"15e. Dataset\"]\n \n # edge definitions with the node IDs\n edge [color = black]\n inla -> stat\n stat -> {zeros, disp, dic,pear} -> {p, zip, nb, zinb} -> sel\n sel -> ext_pred -> coor_pred -> pred -> hotspots -> save\n save -> {mappred, hotspotsb, dics, loc, data}\n\n \n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script> .tiny[.blue[.footnote[ [Modificado de Zuur et al 2017](http://www.highstat.com/index.php/beginner-s-guide-to-regression-models-with-spatial-and-temporal-correlation); [Dzul-Manzanilla et al 2019](http://acaentmex.org/entomologia/revista/2019/EMF/EMF%20497-501.pdf)]]] --- ### **Vigilancia Entomológica con Ovitrampas** <hr style="height:2px;border-width:0;color:#330019;background-color:#330019"> ```r #step 1. load the ovitramps load("C:/Users/HOME/Dropbox/ovitraps_activas&casesmx_klm/8.RData/ovitraps_coordinates.RData") # Step 3. load the localities loc_urb <- rgeomex::loc_inegi19_mx |> sf::st_make_valid() # Step 4. extract the localities with ovitraps loc_urb_ovi <- loc_urb[x,] # Step 5. load the high risk localities y <- readRDS("C:/Users/HOME/OneDrive/proyects/hotspots_paper/8.RData/loc_temp_geocoded.rds") # Step 6. convert th df to sf #### y <- y |> sf::st_as_sf(coords = c("long", "lat"), crs = 4326) # Step 7. extract the localities with high risk with ovitraps #### loc_urb_ovi_hr <- loc_urb_ovi[y, ] # Step 8. load several sf object for maps #### mex_edo <- rgeomex::AGEE_inegi19_mx path <- "C:/Users/HOME/OneDrive/datasets/INEGI/mapa_digital_5.0.A/marco geoestadistico nacional 2010/nacional.shp" mex <- sf::st_read(path, quiet = TRUE) |>